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jianana鐵蟲 (初入文壇)
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[求助]
gromacs 添加新的力場pdb2gmx報(bào)錯
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我現(xiàn)在做一個小分子，gromacs中沒有這個分子的殘基，我的pdb文件如下： HETATM 3 CA LIG 1 4.784 1.069 -0.170 1.00 0.00 C HETATM 4 CA LIG 1 3.605 1.699 -0.680 1.00 0.00 C HETATM 5 HA LIG 1 3.443 2.015 -1.706 1.00 0.00 H HETATM 6 CA LIG 1 2.659 1.795 0.388 1.00 0.00 C HETATM 7 HA LIG 1 1.649 2.180 0.313 1.00 0.00 H HETATM 8 CA LIG 1 4.565 0.777 1.213 1.00 0.00 C HETATM 9 HA LIG 1 5.261 0.271 1.876 1.00 0.00 H HETATM 10 CA LIG 1 3.252 1.226 1.558 1.00 0.00 C HETATM 11 HA LIG 1 2.776 1.123 2.528 1.00 0.00 H HETATM 12 HA LIG 1 5.674 0.822 -0.740 1.00 0.00 H HETATM 13 CA LIG 2 3.580 -1.941 -0.985 1.00 0.00 C HETATM 14 CA LIG 2 2.434 -1.302 -1.537 1.00 0.00 C HETATM 15 HA LIG 2 2.323 -0.937 -2.552 1.00 0.00 H HETATM 16 CA LIG 2 1.442 -1.191 -0.503 1.00 0.00 C HETATM 17 CA LIG 2 3.311 -2.230 0.390 1.00 0.00 C HETATM 18 HA LIG 2 3.999 -2.689 1.093 1.00 0.00 H HETATM 19 CA LIG 2 1.998 -1.768 0.694 1.00 0.00 C HETATM 20 HA LIG 2 1.515 -1.836 1.665 1.00 0.00 H HETATM 21 HA LIG 2 4.511 -2.140 -1.507 1.00 0.00 H HETATM 22 FE LIG 2 3.152 -0.185 0.045 1.00 0.00 Fe HETATM 23 HA LIG 2 0.425 -1.247 -0.870 1.00 0.00 H CONECT 3 12 4 8 CONECT 4 5 3 6 CONECT 5 4 CONECT 6 4 7 10 CONECT 7 6 CONECT 8 3 10 9 CONECT 9 8 CONECT 10 6 8 11 CONECT 11 10 CONECT 12 3 CONECT 13 14 21 17 CONECT 14 15 13 16 CONECT 14 14 CONECT 15 14 23 22 19 CONECT 16 CONECT 17 13 19 18 CONECT 18 17 CONECT 19 16 17 20 CONECT 20 19 CONECT 21 13 CONECT 22 16 CONECT 23 16 MASTER 0 0 0 0 0 0 0 0 21 0 21 0 END 我是在oplsaa.ff中添加的參數(shù)： 1. 在ffbonded.itp中加入 [ bondtypes ] CA CA 1 0.14400 rigid ; the cp ring is a rigid pentagon HA CA 1 0.10800 rigid ; the bonds to hydrogen atoms are always rigid Fe CA 1 0.20600 190.0 ; keep iron between cps (small value to avoid divergence) cp cp 1 0.33200 999900.0 ; keep cps apart (not rigid due to convergence problems) [ angletypes ] CA CA CA 1 108.0 rigid ; keep cp pentagon rigid CA CA HA 1 126.0 292.9 ; in all fecps but decamethylferrocene (cp*) CA xcp xcp 1 90.0 999.9 ; keep cp rings parallel, avoid tilt [ dihedraltypes ] CA CA CA CA 3 rigid ; rigid cp pentagon CA HA CA CA 3 0.0000 0.0000 9.2000 0.0000 0.0000 0.0000 ; improper in all but cp* 2.在atomtypes.atp中添加 opls_966 55.847 ; iron opls_967 12.011 ; carbon in cyclopentadienyl (cp) opls_970 1.008 ; cp hydrogen opls_973 0.001 ;Xcp dummy cp centroid 3. 在ffnonbonded.itp添加 opls_966 Fe 26 55.847 +0.10 A 3.11 2.016 opls_967 CA 6 12.011 -0.10 A 3.55 0.293 opls_970 HA 1 1.008 +0.09 A 2.42 0.126 opls_973 Xcp 0 0.001 0.00 A 0.00 0.000 4 最后，我在aminoacids.rtp中添加殘基【LIG】如下 [ LIG ] [ atoms ] Xcp1 opls_973 0.00 1 Xcp2 opls_973 0.00 1 CA1 opls_967 -0.10 2 HA1 opls_970 0.09 2 CA2 opls_967 -0.10 2 HA2 opls_970 0.09 2 CA3 opls_967 -0.10 2 HA3 opls_970 0.09 2 CA4 opls_967 -0.10 2 HA4 opls_970 0.09 2 CA5 opls_967 -0.10 2 HA5 opls_970 0.09 2 CA6 opls_967 -0.10 2 HA6 opls_970 0.09 2 CA7 opls_967 -0.10 2 HA7 opls_970 0.09 2 CA8 opls_967 -0.10 2 HA8 opls_970 0.09 2 CA9 opls_967 -0.10 2 HA9 opls_970 0.09 2 CA10 opls_967 -0.10 2 HA10 opls_970 0.09 2 FE opls_966 0.10 2 [ bonds ] CA1 FE CA2 FE CA3 FE CA4 FE CA5 FE CA6 FE CA7 FE CA8 FE CA9 FE CA10 FE [ angles ] ; ai aj ak funct CA1 Xcp2 Xcp1 1 CA2 Xcp2 Xcp1 1 CA3 Xcp2 Xcp1 1 CA4 Xcp2 Xcp1 1 CA5 Xcp2 Xcp1 1 CA6 Xcp1 Xcp2 1 CA7 Xcp1 Xcp2 1 CA8 Xcp1 Xcp2 1 CA9 Xcp1 Xcp2 1 CA10 Xcp1 Xcp2 1 CA5 CA1 HA1 1 CA2 CA1 HA1 1 CA1 CA2 HA2 1 CA3 CA2 HA2 1 CA2 CA3 HA3 1 CA4 CA3 HA3 1 CA3 CA4 HA4 1 CA5 CA4 HA4 1 CA4 CA5 HA5 1 CA1 CA5 HA5 1 CA10 CA6 HA6 1 CA7 CA6 HA6 1 CA6 CA7 HA7 1 CA8 CA7 HA7 1 CA7 CA8 HA8 1 CA9 CA8 HA8 1 CA8 CA9 HA9 1 CA10 CA9 HA9 1 CA9 CA10 HA10 1 CA6 CA10 HA10 1 [ dihedrals ] ; ai aj ak al funct CA1 Xcp2 Xcp1 CA6 3 CA2 Xcp2 Xcp1 CA6 3 CA3 Xcp2 Xcp1 CA6 3 CA4 Xcp2 Xcp1 CA6 3 CA5 Xcp2 Xcp1 CA6 3 CA1 Xcp2 Xcp1 CA7 3 CA2 Xcp2 Xcp1 CA7 3 CA3 Xcp2 Xcp1 CA7 3 CA4 Xcp2 Xcp1 CA7 3 CA5 Xcp2 Xcp1 CA7 3 CA1 Xcp2 Xcp1 CA8 3 CA2 Xcp2 Xcp1 CA8 3 CA3 Xcp2 Xcp1 CA8 3 CA4 Xcp2 Xcp1 CA8 3 CA5 Xcp2 Xcp1 CA8 3 CA1 Xcp2 Xcp1 CA9 3 CA2 Xcp2 Xcp1 CA9 3 CA3 Xcp2 Xcp1 CA9 3 CA4 Xcp2 Xcp1 CA9 3 CA5 Xcp2 Xcp1 CA9 3 CA1 Xcp2 Xcp1 CA10 3 CA2 Xcp2 Xcp1 CA10 3 CA3 Xcp2 Xcp1 CA10 3 CA4 Xcp2 Xcp1 CA10 3 CA5 Xcp2 Xcp1 CA10 3 HA1 CA1 CA2 HA2 3 HA1 CA1 CA2 CA3 3 CA5 CA1 CA2 HA2 3 HA2 CA2 CA3 HA3 3 HA2 CA2 CA3 CA4 3 CA1 CA2 CA3 HA3 3 HA3 CA3 CA4 HA4 3 HA3 CA3 CA4 CA5 3 CA2 CA3 CA4 HA4 3 HA4 CA4 CA5 HA5 3 HA4 CA4 CA5 CA1 3 CA3 CA4 CA5 HA5 3 HA5 CA5 CA1 HA1 3 HA5 CA5 CA1 CA2 3 CA4 CA5 CA1 HA1 3 HA6 CA6 CA7 HA7 3 HA6 CA6 CA7 CA8 3 CA10 CA6 CA7 HA7 3 HA7 CA7 CA8 HA8 3 HA7 CA7 CA8 CA9 3 CA6 CA7 CA8 HA8 3 HA8 CA8 CA9 HA9 3 HA8 CA8 CA9 CA10 3 CA7 CA8 CA9 HA9 3 HA9 CA9 CA10 HA10 3 HA9 CA9 CA10 CA6 3 CA8 CA9 CA10 HA10 3 HA10 CA10 CA6 HA6 3 HA10 CA10 CA6 CA7 3 CA9 CA10 CA6 HA6 3 [ impropers ] ; ai aj ak al funct c0 CA1 HA1 CA2 CA5 1 improper_CA_HA_CA_CA CA1 HA1 CA5 CA3 1 improper_CA_HA_CA_CA CA2 HA2 CA3 CA1 1 improper_CA_HA_CA_CA CA2 HA2 CA1 CA3 1 improper_CA_HA_CA_CA CA3 HA3 CA4 CA2 1 improper_CA_HA_CA_CA CA3 HA3 CA2 CA4 1 improper_CA_HA_CA_CA CA4 HA4 CA5 CA3 1 improper_CA_HA_CA_CA CA4 HA4 CA3 CA5 1 improper_CA_HA_CA_CA CA5 HA5 CA1 CA4 1 improper_CA_HA_CA_CA CA5 HA5 CA4 CA1 1 improper_CA_HA_CA_CA CA6 HA6 CA7 CA10 1 improper_CA_HA_CA_CA CA6 HA6 CA10 CA7 1 improper_CA_HA_CA_CA CA7 HA7 CA8 CA6 1 improper_CA_HA_CA_CA CA7 HA7 CA6 CA8 1 improper_CA_HA_CA_CA CA8 HA8 CA9 CA7 1 improper_CA_HA_CA_CA CA8 HA8 CA7 CA9 1 improper_CA_HA_CA_CA CA9 HA9 CA10 CA8 1 improper_CA_HA_CA_CA CA9 HA9 CA8 CA10 1 improper_CA_HA_CA_CA CA10 HA10 CA6 CA9 1 improper_CA_HA_CA_CA CA10 HA10 CA9 CA6 1 improper_CA_HA_CA_CA 現(xiàn)在我運(yùn)行pdb2gmx -f *.pdb -o *.gro -p *.top命令出錯 Back Off! I just backed up ferrocene.top to ./#ferrocene.top.3# Processing chain 1 (23 atoms, 2 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Warning: Starting residue LIG1 in chain not identified as Protein/RNA/DNA. Warning: Starting residue LIG2 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully ------------------------------------------------------- Program pdb2gmx, VERSION 4.5.4 Source code file: pdb2gmx.c, line: 655 Fatal error: Atom cp in residue LIG 1 was not found in rtp entry LIG with 23 atoms while sorting atoms. . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors 請問大家，這是什么原因呢？寫這個力場已經(jīng)用了我快一個月的時間了，到現(xiàn)在還是不對，都快崩潰了！希望大家?guī)蛶兔Π�！在此謝過！ |
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